Contacts of the strand formed by residues 1041 - 1047 (chain A) in PDB entry 1D1Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A TYR* 3.5 41.3 + + - -
1031A LEU* 3.9 24.2 - - + -
1032A ARG 3.3 11.7 - - - +
1033A ASP* 3.6 10.5 - - - -
1034A SER 4.0 0.2 - - - +
1039A GLY* 3.6 20.2 + - - -
1040A VAL* 1.3 82.7 - - - +
1042A CYS* 1.3 63.7 - - - +
1055A ARG* 3.4 5.9 - - - -
1056A VAL* 2.8 44.4 + - + +
1057A SER* 5.1 0.2 - - - -
1058A GLN* 5.9 0.4 - - + -
1064A TRP* 3.9 31.9 - + - -
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Residues in contact with CYS1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031A LEU* 3.4 6.4 - - - -
1032A ARG* 2.8 57.4 + - + -
1034A SER* 3.9 14.4 - - - -
1041A TYR* 1.3 79.2 - - - +
1043A LEU* 1.3 61.6 - - - +
1044A CYS* 3.6 5.3 - - - -
1053A THR* 3.6 20.2 - - + -
1054A TYR 3.6 3.4 - - - -
1055A ARG* 3.9 16.6 - - - -
5001A SO4 3.8 23.3 - - - -
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Residues in contact with LEU1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A TYR* 4.1 11.2 - - + -
1030A LEU 3.6 13.9 - - - +
1031A LEU* 3.8 6.4 - - + +
1041A TYR 4.1 0.2 - - - -
1042A CYS* 1.3 71.1 - - - +
1044A CYS* 1.3 60.6 + - - +
1045A VAL* 4.3 6.3 - - + -
1052A TYR 3.5 1.9 - - - +
1053A THR* 3.4 2.8 - - - -
1054A TYR* 2.8 56.0 + - + +
1056A VAL* 3.8 20.4 - - + +
1066A ALA* 5.4 2.5 - - + -
1083A LEU* 5.0 3.6 - - + -
1084A ILE* 4.0 25.6 - - + -
1087A PHE* 4.9 10.1 - - + -
1094A ILE* 4.9 8.1 - - + -
1098A LEU* 4.0 31.9 - - + -
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Residues in contact with CYS1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016A GLY 6.2 0.7 - - - -
1017A GLU* 5.7 2.9 - - + -
1020A LEU* 3.5 21.3 - - + +
1029A TYR* 3.1 6.8 - - - +
1030A LEU* 2.8 39.1 + - + +
1032A ARG* 3.4 33.4 - - - -
1042A CYS* 3.6 20.9 - - - -
1043A LEU* 1.3 74.7 - - - +
1045A VAL* 1.3 61.6 + - - +
1051A ILE* 4.0 9.6 - - + -
1052A TYR 3.4 4.9 - - - -
1053A THR* 4.1 11.7 - - - -
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Residues in contact with VAL1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020A LEU* 4.6 0.2 - - - -
1027A GLY* 4.2 6.5 - - - -
1028A SER 3.4 10.1 - - - +
1029A TYR* 4.2 0.7 - - + -
1043A LEU* 4.3 8.1 - - + -
1044A CYS* 1.3 79.9 - - - +
1046A LEU* 1.3 65.8 + - - +
1050A TYR 3.6 0.3 - - - +
1051A ILE* 3.4 5.8 - - - -
1052A TYR* 2.8 46.5 + - + +
1054A TYR* 4.2 18.4 - - + -
1094A ILE* 4.5 2.7 - - + -
1095A VAL* 4.8 2.7 - - + -
1096A ILE* 3.8 34.8 - - + +
1098A LEU* 3.4 30.7 - - + -
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Residues in contact with LEU1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020A LEU* 3.5 24.6 - - + +
1021A LEU* 3.8 16.4 - - + +
1023A THR* 3.9 0.9 - - - +
1024A GLY* 3.8 9.0 - - - +
1025A LEU 3.4 38.6 - - - +
1026A ASP* 3.5 1.5 - - - +
1027A GLY* 2.8 29.1 + - - -
1028A SER* 3.0 16.0 + - - +
1045A VAL* 1.3 73.4 - - - +
1047A TYR* 1.3 67.6 + - - +
1049A GLY* 3.8 9.2 - - - +
1050A TYR 3.4 28.0 - - - +
1051A ILE* 3.5 22.2 - - + +
1096A ILE* 4.0 0.3 - - - +
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Residues in contact with TYR1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A ASP* 3.7 5.4 - - - -
1045A VAL 3.8 0.2 + - - -
1046A LEU* 1.3 79.1 - - - +
1048A HIS* 1.3 114.1 + + + +
1049A GLY 3.2 0.9 - - - -
1050A TYR* 2.9 21.8 + - - +
1052A TYR* 3.5 28.7 + - + -
1095A VAL* 3.4 41.7 - - + -
1096A ILE* 3.9 34.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il